OpenMS
2.5.0
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Shows basic information about the data in an OpenMS readable file.
pot. predecessor tools | FileInfo | pot. successor tools |
any tool operating on MS peak data (in mzML format) | none ; console or text file |
This tool can show basic information about the data in several peak, feature and consensus feature files. It can
The command line parameters of this tool are:
FileInfo -- Shows basic information about the file, such as data ranges and file type. Full documentation: http://www.openms.de/documentation/TOPP_FileInfo.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. Usage: FileInfo <options> Options (mandatory options marked with '*'): -in <file>* Input file (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXM L', 'consensusXML', 'idXML', 'pepXML', 'fid', 'mzid', 'trafoXML', 'fasta') -in_type <type> Input file type -- default: determined from file extension or content (valid: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'idXML', 'pepXML', 'fid', 'mzid', 'trafoXML') -out <file> Optional output file. If left out, the output is written to the command line. (valid formats: 'txt') -m Show meta information about the whole experiment -p Shows data processing information -s Computes a five-number statistics of intensities, qualities, and widths -d Show detailed listing of all spectra and chromatograms (peak files only) -c Check for corrupt data in the file (peak files only) -v Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML ) -i Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard) Common TOPP options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced)
INI file documentation of this tool:
In order to enrich the resulting data of your analysis pipeline or to quickly compare different outcomes of your pipeline you can invoke the aforementioned information of your input data and (intermediary) results.